[Chimera-users] write selected command

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 1 13:11:01 PDT 2009

Hi Ed,
The "write" command only allows you to save one model at a time.

To save multiple models to one PDB file you have to use the GUI  
("File... Save PDB" or "Actions... Write PDB").

Sorry about that,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote:

> Elaine and co,
> I have a mess of models that I'm opening, repositioning a ligand  
> using match to various positions in each model. No problem there.  
> For each model and ligand position I select the correct chains from  
> that model with the repositioned ligand models but can't manage to  
> save coordinates. Obviously there's the save pdb dialog but for all  
> these models and ligands this will be more convenient scripted into  
> chimera commands. I've got it all working except this:
> select #6:.a-p #8 #9
> write selected relative 0 #6,8,9 /path/to/file.pdb
> ~select
> The part it doesn't like is the model_numbers and I've tried  
> various permutations without success. The only way I can get it to  
> work is if I only specify one model number.
> Can you please help me figure out how to phrase this command  
> correctly? An example or two on that commands page might make the  
> syntax easier to decipher.
> Thank you for your excellent program and support.
> Ed
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Edward Brignole
> NIH Kirschstein Postdoctoral Fellow
> Francisco Asturias Lab, CB227
> Center for Integrative Molecular Biosciences
> The Scripps Research Institute
> www.scripps.edu/~brignole
> brignole at scripps.edu
> 443-653-2070 (cell)
> 858-784-8598 (lab)
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